Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_020922563.1 RHE_RS20615 homoserine O-succinyltransferase
Query= SwissProt::Q7CWE8 (308 letters) >NCBI__GCF_000092045.1:WP_020922563.1 Length = 307 Score = 565 bits (1457), Expect = e-166 Identities = 267/304 (87%), Positives = 283/304 (93%) Query: 1 MPIKIPDTLPAFETLVHEGVRVMTETAAIRQDIRPLQIGLLNLMPNKIKTEIQMARLVGA 60 MPIKIPDTLPAFETLV EGVRVMTET AIRQDIRPLQIGLLNLMPNKIKTE+QMARLVGA Sbjct: 1 MPIKIPDTLPAFETLVQEGVRVMTETMAIRQDIRPLQIGLLNLMPNKIKTELQMARLVGA 60 Query: 61 SPLQVELSLIRIGGHRAKNTPEEHLLSFYQTWEEVRHRKFDGFIITGAPIELLDYEDVTY 120 SPLQVELSLIRIGGH+AKNT E+HLL+FYQTWEEV+ RKFDGFIITGAPIELL YEDVTY Sbjct: 61 SPLQVELSLIRIGGHKAKNTSEDHLLAFYQTWEEVKQRKFDGFIITGAPIELLPYEDVTY 120 Query: 121 WNEMQQIFEWTQTNVHSTLNVCWGAMAAIYHFHGVPKYELKEKAFGVYRHRNLSPSSIYL 180 W EMQ+IF WT+TNVHST+NVCWGAMAAIYHFHGVPKYELKEKAFGVYRHRNL PSSIYL Sbjct: 121 WAEMQEIFNWTETNVHSTMNVCWGAMAAIYHFHGVPKYELKEKAFGVYRHRNLKPSSIYL 180 Query: 181 NGFSDDFQVPVSRWTEVRRADIEKHPELEILMESDEMGVCLAHEKAGNRLYMFNHVEYDS 240 NGFSD+F+VPVSRWTEVRR DIEK LEILMES EMGVCL HEK G RLYMFNHVEYDS Sbjct: 181 NGFSDNFEVPVSRWTEVRREDIEKSASLEILMESSEMGVCLVHEKRGRRLYMFNHVEYDS 240 Query: 241 TSLADEYFRDVNSGVPIKLPHDYFPHNDPELAPLNRWRSHAHLFFGNWINEIYQTTPYDP 300 TSL+DEYFRDV++GVPIK+PH+YFPHNDP LAP NRWRSHAHL FGNWINEIYQTTPYD Sbjct: 241 TSLSDEYFRDVDAGVPIKMPHNYFPHNDPTLAPQNRWRSHAHLLFGNWINEIYQTTPYDV 300 Query: 301 QAIG 304 + IG Sbjct: 301 EEIG 304 Lambda K H 0.321 0.137 0.429 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 462 Number of extensions: 12 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 307 Length adjustment: 27 Effective length of query: 281 Effective length of database: 280 Effective search space: 78680 Effective search space used: 78680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory